Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in report_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-11-28, 18:46 based on data in: /corral4/main/jobs/053/991/53991775/working/multiqc_WDir


        General Statistics

        Showing 336/336 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        1605qcpar23_S137_L001_R1_001_fastq_gz
        85.9%
        53%
        131 bp
        0.0
        1605qcpar23_S137_L001_R2_001_fastq_gz
        83.6%
        53%
        131 bp
        0.0
        1605qcpar23_S137_L002_R1_001_fastq_gz
        85.9%
        53%
        131 bp
        0.0
        1605qcpar23_S137_L002_R2_001_fastq_gz
        83.0%
        53%
        132 bp
        0.0
        1605qcpar23_S137_L003_R1_001_fastq_gz
        85.9%
        53%
        131 bp
        0.0
        1605qcpar23_S137_L003_R2_001_fastq_gz
        83.7%
        53%
        131 bp
        0.0
        1605qcpar23_S137_L004_R1_001_fastq_gz
        86.1%
        53%
        131 bp
        0.0
        1605qcpar23_S137_L004_R2_001_fastq_gz
        83.3%
        53%
        131 bp
        0.0
        1640qcpar23_S138_L001_R1_001_fastq_gz
        86.1%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L001_R2_001_fastq_gz
        82.7%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L002_R1_001_fastq_gz
        85.8%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L002_R2_001_fastq_gz
        82.8%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L003_R1_001_fastq_gz
        86.1%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L003_R2_001_fastq_gz
        83.4%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L004_R1_001_fastq_gz
        85.8%
        48%
        144 bp
        0.1
        1640qcpar23_S138_L004_R2_001_fastq_gz
        82.7%
        48%
        144 bp
        0.1
        2412qcpar23_S136_L001_R1_001_fastq_gz
        88.4%
        52%
        138 bp
        0.1
        2412qcpar23_S136_L001_R2_001_fastq_gz
        85.6%
        52%
        139 bp
        0.1
        2412qcpar23_S136_L002_R1_001_fastq_gz
        88.2%
        52%
        138 bp
        0.1
        2412qcpar23_S136_L002_R2_001_fastq_gz
        85.1%
        52%
        139 bp
        0.1
        2412qcpar23_S136_L003_R1_001_fastq_gz
        88.4%
        52%
        138 bp
        0.1
        2412qcpar23_S136_L003_R2_001_fastq_gz
        85.8%
        52%
        139 bp
        0.1
        2412qcpar23_S136_L004_R1_001_fastq_gz
        88.3%
        52%
        138 bp
        0.1
        2412qcpar23_S136_L004_R2_001_fastq_gz
        85.5%
        52%
        139 bp
        0.1
        3453par23_S97_L001_R1_001_fastq_gz
        90.9%
        50%
        140 bp
        0.7
        3453par23_S97_L001_R2_001_fastq_gz
        89.0%
        50%
        140 bp
        0.7
        3453par23_S97_L002_R1_001_fastq_gz
        90.8%
        50%
        140 bp
        0.7
        3453par23_S97_L002_R2_001_fastq_gz
        88.6%
        50%
        140 bp
        0.7
        3453par23_S97_L003_R1_001_fastq_gz
        91.0%
        50%
        140 bp
        0.8
        3453par23_S97_L003_R2_001_fastq_gz
        89.3%
        50%
        140 bp
        0.8
        3453par23_S97_L004_R1_001_fastq_gz
        90.9%
        50%
        140 bp
        0.7
        3453par23_S97_L004_R2_001_fastq_gz
        88.8%
        50%
        140 bp
        0.7
        3454par23_S98_L001_R1_001_fastq_gz
        90.3%
        52%
        146 bp
        0.3
        3454par23_S98_L001_R2_001_fastq_gz
        87.2%
        52%
        146 bp
        0.3
        3454par23_S98_L002_R1_001_fastq_gz
        90.0%
        52%
        146 bp
        0.2
        3454par23_S98_L002_R2_001_fastq_gz
        86.9%
        52%
        147 bp
        0.2
        3454par23_S98_L003_R1_001_fastq_gz
        90.3%
        52%
        146 bp
        0.3
        3454par23_S98_L003_R2_001_fastq_gz
        87.6%
        52%
        146 bp
        0.3
        3454par23_S98_L004_R1_001_fastq_gz
        90.1%
        52%
        146 bp
        0.3
        3454par23_S98_L004_R2_001_fastq_gz
        86.9%
        52%
        147 bp
        0.3
        3455par23_S99_L001_R1_001_fastq_gz
        89.0%
        52%
        146 bp
        0.3
        3455par23_S99_L001_R2_001_fastq_gz
        87.1%
        52%
        146 bp
        0.3
        3455par23_S99_L002_R1_001_fastq_gz
        88.9%
        52%
        146 bp
        0.2
        3455par23_S99_L002_R2_001_fastq_gz
        86.8%
        52%
        146 bp
        0.2
        3455par23_S99_L003_R1_001_fastq_gz
        89.1%
        52%
        146 bp
        0.3
        3455par23_S99_L003_R2_001_fastq_gz
        87.4%
        52%
        146 bp
        0.3
        3455par23_S99_L004_R1_001_fastq_gz
        89.1%
        52%
        146 bp
        0.2
        3455par23_S99_L004_R2_001_fastq_gz
        87.0%
        52%
        146 bp
        0.2
        3456par23_S100_L001_R1_001_fastq_gz
        90.3%
        50%
        147 bp
        0.4
        3456par23_S100_L001_R2_001_fastq_gz
        87.9%
        50%
        147 bp
        0.4
        3456par23_S100_L002_R1_001_fastq_gz
        90.2%
        50%
        147 bp
        0.4
        3456par23_S100_L002_R2_001_fastq_gz
        87.5%
        50%
        147 bp
        0.4
        3456par23_S100_L003_R1_001_fastq_gz
        90.5%
        51%
        147 bp
        0.4
        3456par23_S100_L003_R2_001_fastq_gz
        88.3%
        50%
        147 bp
        0.4
        3456par23_S100_L004_R1_001_fastq_gz
        90.3%
        50%
        147 bp
        0.4
        3456par23_S100_L004_R2_001_fastq_gz
        87.6%
        50%
        147 bp
        0.4
        3457par23_S101_L001_R1_001_fastq_gz
        91.3%
        51%
        145 bp
        0.6
        3457par23_S101_L001_R2_001_fastq_gz
        89.3%
        51%
        145 bp
        0.6
        3457par23_S101_L002_R1_001_fastq_gz
        91.1%
        51%
        145 bp
        0.6
        3457par23_S101_L002_R2_001_fastq_gz
        89.0%
        51%
        145 bp
        0.6
        3457par23_S101_L003_R1_001_fastq_gz
        91.4%
        51%
        145 bp
        0.7
        3457par23_S101_L003_R2_001_fastq_gz
        89.6%
        51%
        145 bp
        0.7
        3457par23_S101_L004_R1_001_fastq_gz
        91.2%
        51%
        145 bp
        0.6
        3457par23_S101_L004_R2_001_fastq_gz
        89.1%
        51%
        145 bp
        0.6
        3458par23_S102_L001_R1_001_fastq_gz
        94.7%
        57%
        146 bp
        0.8
        3458par23_S102_L001_R2_001_fastq_gz
        92.9%
        57%
        146 bp
        0.8
        3458par23_S102_L002_R1_001_fastq_gz
        94.6%
        57%
        146 bp
        0.7
        3458par23_S102_L002_R2_001_fastq_gz
        92.7%
        57%
        146 bp
        0.7
        3458par23_S102_L003_R1_001_fastq_gz
        94.8%
        58%
        146 bp
        0.8
        3458par23_S102_L003_R2_001_fastq_gz
        93.2%
        57%
        146 bp
        0.8
        3458par23_S102_L004_R1_001_fastq_gz
        94.8%
        57%
        146 bp
        0.7
        3458par23_S102_L004_R2_001_fastq_gz
        92.7%
        57%
        146 bp
        0.7
        3459par23_S103_L001_R1_001_fastq_gz
        92.0%
        51%
        148 bp
        0.6
        3459par23_S103_L001_R2_001_fastq_gz
        89.8%
        51%
        148 bp
        0.6
        3459par23_S103_L002_R1_001_fastq_gz
        91.9%
        51%
        148 bp
        0.5
        3459par23_S103_L002_R2_001_fastq_gz
        89.6%
        51%
        148 bp
        0.5
        3459par23_S103_L003_R1_001_fastq_gz
        92.2%
        51%
        148 bp
        0.6
        3459par23_S103_L003_R2_001_fastq_gz
        90.1%
        51%
        148 bp
        0.6
        3459par23_S103_L004_R1_001_fastq_gz
        92.0%
        51%
        148 bp
        0.5
        3459par23_S103_L004_R2_001_fastq_gz
        89.7%
        51%
        148 bp
        0.5
        3460par23_S104_L001_R1_001_fastq_gz
        85.4%
        55%
        117 bp
        0.1
        3460par23_S104_L001_R2_001_fastq_gz
        83.8%
        54%
        117 bp
        0.1
        3460par23_S104_L002_R1_001_fastq_gz
        85.2%
        55%
        117 bp
        0.1
        3460par23_S104_L002_R2_001_fastq_gz
        83.3%
        54%
        118 bp
        0.1
        3460par23_S104_L003_R1_001_fastq_gz
        85.7%
        55%
        117 bp
        0.2
        3460par23_S104_L003_R2_001_fastq_gz
        84.1%
        55%
        118 bp
        0.2
        3460par23_S104_L004_R1_001_fastq_gz
        85.4%
        55%
        117 bp
        0.1
        3460par23_S104_L004_R2_001_fastq_gz
        83.4%
        54%
        117 bp
        0.1
        3461par23_S105_L001_R1_001_fastq_gz
        81.5%
        52%
        94 bp
        0.2
        3461par23_S105_L001_R2_001_fastq_gz
        79.0%
        51%
        96 bp
        0.2
        3461par23_S105_L002_R1_001_fastq_gz
        81.1%
        52%
        95 bp
        0.2
        3461par23_S105_L002_R2_001_fastq_gz
        78.6%
        51%
        96 bp
        0.2
        3461par23_S105_L003_R1_001_fastq_gz
        81.5%
        52%
        95 bp
        0.2
        3461par23_S105_L003_R2_001_fastq_gz
        79.5%
        52%
        96 bp
        0.2
        3461par23_S105_L004_R1_001_fastq_gz
        81.4%
        52%
        94 bp
        0.2
        3461par23_S105_L004_R2_001_fastq_gz
        79.0%
        51%
        96 bp
        0.2
        3462par23_S106_L001_R1_001_fastq_gz
        90.4%
        54%
        144 bp
        0.4
        3462par23_S106_L001_R2_001_fastq_gz
        86.3%
        53%
        144 bp
        0.4
        3462par23_S106_L002_R1_001_fastq_gz
        90.2%
        54%
        144 bp
        0.3
        3462par23_S106_L002_R2_001_fastq_gz
        86.3%
        53%
        144 bp
        0.3
        3462par23_S106_L003_R1_001_fastq_gz
        90.4%
        54%
        144 bp
        0.4
        3462par23_S106_L003_R2_001_fastq_gz
        87.0%
        53%
        144 bp
        0.4
        3462par23_S106_L004_R1_001_fastq_gz
        90.3%
        54%
        144 bp
        0.4
        3462par23_S106_L004_R2_001_fastq_gz
        86.4%
        53%
        144 bp
        0.4
        3473par23_S107_L001_R1_001_fastq_gz
        57.9%
        55%
        76 bp
        0.0
        3473par23_S107_L001_R2_001_fastq_gz
        56.1%
        54%
        78 bp
        0.0
        3473par23_S107_L002_R1_001_fastq_gz
        57.6%
        54%
        76 bp
        0.0
        3473par23_S107_L002_R2_001_fastq_gz
        56.4%
        54%
        78 bp
        0.0
        3473par23_S107_L003_R1_001_fastq_gz
        58.6%
        55%
        77 bp
        0.0
        3473par23_S107_L003_R2_001_fastq_gz
        57.0%
        55%
        79 bp
        0.0
        3473par23_S107_L004_R1_001_fastq_gz
        57.7%
        55%
        76 bp
        0.0
        3473par23_S107_L004_R2_001_fastq_gz
        55.6%
        54%
        78 bp
        0.0
        3474par23_S108_L001_R1_001_fastq_gz
        87.5%
        52%
        142 bp
        0.2
        3474par23_S108_L001_R2_001_fastq_gz
        85.0%
        52%
        143 bp
        0.2
        3474par23_S108_L002_R1_001_fastq_gz
        87.4%
        52%
        142 bp
        0.2
        3474par23_S108_L002_R2_001_fastq_gz
        84.8%
        52%
        143 bp
        0.2
        3474par23_S108_L003_R1_001_fastq_gz
        87.7%
        52%
        142 bp
        0.2
        3474par23_S108_L003_R2_001_fastq_gz
        85.5%
        52%
        143 bp
        0.2
        3474par23_S108_L004_R1_001_fastq_gz
        87.5%
        52%
        142 bp
        0.2
        3474par23_S108_L004_R2_001_fastq_gz
        84.9%
        52%
        143 bp
        0.2
        3475par23_S109_L001_R1_001_fastq_gz
        91.3%
        52%
        144 bp
        0.6
        3475par23_S109_L001_R2_001_fastq_gz
        88.7%
        51%
        144 bp
        0.6
        3475par23_S109_L002_R1_001_fastq_gz
        91.2%
        52%
        144 bp
        0.5
        3475par23_S109_L002_R2_001_fastq_gz
        88.5%
        51%
        144 bp
        0.5
        3475par23_S109_L003_R1_001_fastq_gz
        91.4%
        52%
        144 bp
        0.6
        3475par23_S109_L003_R2_001_fastq_gz
        89.1%
        52%
        144 bp
        0.6
        3475par23_S109_L004_R1_001_fastq_gz
        91.2%
        52%
        144 bp
        0.5
        3475par23_S109_L004_R2_001_fastq_gz
        88.5%
        51%
        144 bp
        0.5
        3476par23_S110_L001_R1_001_fastq_gz
        93.0%
        51%
        147 bp
        0.8
        3476par23_S110_L001_R2_001_fastq_gz
        90.4%
        51%
        147 bp
        0.8
        3476par23_S110_L002_R1_001_fastq_gz
        92.9%
        51%
        147 bp
        0.8
        3476par23_S110_L002_R2_001_fastq_gz
        90.2%
        51%
        147 bp
        0.8
        3476par23_S110_L003_R1_001_fastq_gz
        93.1%
        51%
        147 bp
        0.8
        3476par23_S110_L003_R2_001_fastq_gz
        90.8%
        51%
        147 bp
        0.8
        3476par23_S110_L004_R1_001_fastq_gz
        93.0%
        51%
        147 bp
        0.8
        3476par23_S110_L004_R2_001_fastq_gz
        90.3%
        51%
        147 bp
        0.8
        3477par23_S111_L001_R1_001_fastq_gz
        75.9%
        51%
        120 bp
        0.0
        3477par23_S111_L001_R2_001_fastq_gz
        72.7%
        51%
        121 bp
        0.0
        3477par23_S111_L002_R1_001_fastq_gz
        75.3%
        51%
        121 bp
        0.0
        3477par23_S111_L002_R2_001_fastq_gz
        72.5%
        51%
        121 bp
        0.0
        3477par23_S111_L003_R1_001_fastq_gz
        75.9%
        51%
        121 bp
        0.0
        3477par23_S111_L003_R2_001_fastq_gz
        73.4%
        51%
        121 bp
        0.0
        3477par23_S111_L004_R1_001_fastq_gz
        75.6%
        51%
        120 bp
        0.0
        3477par23_S111_L004_R2_001_fastq_gz
        73.0%
        51%
        121 bp
        0.0
        3478par23_S112_L001_R1_001_fastq_gz
        89.5%
        51%
        138 bp
        0.5
        3478par23_S112_L001_R2_001_fastq_gz
        86.6%
        51%
        138 bp
        0.5
        3478par23_S112_L002_R1_001_fastq_gz
        89.3%
        51%
        138 bp
        0.5
        3478par23_S112_L002_R2_001_fastq_gz
        86.4%
        51%
        138 bp
        0.5
        3478par23_S112_L003_R1_001_fastq_gz
        89.6%
        51%
        138 bp
        0.5
        3478par23_S112_L003_R2_001_fastq_gz
        87.1%
        51%
        138 bp
        0.5
        3478par23_S112_L004_R1_001_fastq_gz
        89.4%
        51%
        138 bp
        0.5
        3478par23_S112_L004_R2_001_fastq_gz
        86.5%
        51%
        138 bp
        0.5
        3479par23_S113_L001_R1_001_fastq_gz
        92.2%
        50%
        148 bp
        0.6
        3479par23_S113_L001_R2_001_fastq_gz
        89.3%
        50%
        148 bp
        0.6
        3479par23_S113_L002_R1_001_fastq_gz
        92.0%
        50%
        148 bp
        0.6
        3479par23_S113_L002_R2_001_fastq_gz
        88.9%
        50%
        148 bp
        0.6
        3479par23_S113_L003_R1_001_fastq_gz
        92.3%
        50%
        148 bp
        0.6
        3479par23_S113_L003_R2_001_fastq_gz
        89.5%
        50%
        148 bp
        0.6
        3479par23_S113_L004_R1_001_fastq_gz
        92.2%
        50%
        148 bp
        0.6
        3479par23_S113_L004_R2_001_fastq_gz
        89.0%
        50%
        148 bp
        0.6
        3480par23_S114_L001_R1_001_fastq_gz
        86.9%
        48%
        127 bp
        0.2
        3480par23_S114_L001_R2_001_fastq_gz
        83.8%
        48%
        128 bp
        0.2
        3480par23_S114_L002_R1_001_fastq_gz
        86.6%
        48%
        127 bp
        0.2
        3480par23_S114_L002_R2_001_fastq_gz
        83.6%
        48%
        128 bp
        0.2
        3480par23_S114_L003_R1_001_fastq_gz
        86.8%
        48%
        127 bp
        0.2
        3480par23_S114_L003_R2_001_fastq_gz
        84.3%
        48%
        128 bp
        0.2
        3480par23_S114_L004_R1_001_fastq_gz
        86.7%
        48%
        127 bp
        0.2
        3480par23_S114_L004_R2_001_fastq_gz
        83.8%
        48%
        128 bp
        0.2
        3514par23_S115_L001_R1_001_fastq_gz
        92.2%
        53%
        147 bp
        0.6
        3514par23_S115_L001_R2_001_fastq_gz
        89.6%
        53%
        147 bp
        0.6
        3514par23_S115_L002_R1_001_fastq_gz
        92.1%
        53%
        147 bp
        0.6
        3514par23_S115_L002_R2_001_fastq_gz
        89.4%
        53%
        147 bp
        0.6
        3514par23_S115_L003_R1_001_fastq_gz
        92.3%
        53%
        147 bp
        0.6
        3514par23_S115_L003_R2_001_fastq_gz
        90.0%
        53%
        147 bp
        0.6
        3514par23_S115_L004_R1_001_fastq_gz
        92.2%
        53%
        147 bp
        0.6
        3514par23_S115_L004_R2_001_fastq_gz
        89.4%
        53%
        147 bp
        0.6
        3515par23_S116_L001_R1_001_fastq_gz
        89.1%
        55%
        144 bp
        0.2
        3515par23_S116_L001_R2_001_fastq_gz
        86.4%
        54%
        144 bp
        0.2
        3515par23_S116_L002_R1_001_fastq_gz
        88.9%
        55%
        144 bp
        0.1
        3515par23_S116_L002_R2_001_fastq_gz
        86.2%
        55%
        144 bp
        0.1
        3515par23_S116_L003_R1_001_fastq_gz
        89.4%
        55%
        144 bp
        0.2
        3515par23_S116_L003_R2_001_fastq_gz
        86.9%
        55%
        144 bp
        0.2
        3515par23_S116_L004_R1_001_fastq_gz
        89.1%
        55%
        144 bp
        0.2
        3515par23_S116_L004_R2_001_fastq_gz
        86.1%
        54%
        144 bp
        0.2
        3516par23_S117_L001_R1_001_fastq_gz
        91.7%
        53%
        147 bp
        0.5
        3516par23_S117_L001_R2_001_fastq_gz
        89.1%
        52%
        147 bp
        0.5
        3516par23_S117_L002_R1_001_fastq_gz
        91.6%
        53%
        147 bp
        0.5
        3516par23_S117_L002_R2_001_fastq_gz
        88.9%
        53%
        147 bp
        0.5
        3516par23_S117_L003_R1_001_fastq_gz
        91.9%
        53%
        147 bp
        0.5
        3516par23_S117_L003_R2_001_fastq_gz
        89.5%
        53%
        147 bp
        0.5
        3516par23_S117_L004_R1_001_fastq_gz
        91.7%
        53%
        147 bp
        0.5
        3516par23_S117_L004_R2_001_fastq_gz
        88.9%
        53%
        147 bp
        0.5
        3517par23_S118_L001_R1_001_fastq_gz
        91.2%
        55%
        145 bp
        0.3
        3517par23_S118_L001_R2_001_fastq_gz
        88.5%
        55%
        145 bp
        0.3
        3517par23_S118_L002_R1_001_fastq_gz
        91.1%
        55%
        145 bp
        0.3
        3517par23_S118_L002_R2_001_fastq_gz
        88.4%
        55%
        145 bp
        0.3
        3517par23_S118_L003_R1_001_fastq_gz
        91.3%
        55%
        145 bp
        0.3
        3517par23_S118_L003_R2_001_fastq_gz
        89.1%
        55%
        145 bp
        0.3
        3517par23_S118_L004_R1_001_fastq_gz
        91.1%
        55%
        145 bp
        0.3
        3517par23_S118_L004_R2_001_fastq_gz
        88.5%
        55%
        145 bp
        0.3
        3518par23_S120_L001_R1_001_fastq_gz
        89.8%
        53%
        140 bp
        0.4
        3518par23_S120_L001_R2_001_fastq_gz
        87.3%
        53%
        141 bp
        0.4
        3518par23_S120_L002_R1_001_fastq_gz
        89.8%
        53%
        141 bp
        0.3
        3518par23_S120_L002_R2_001_fastq_gz
        87.1%
        53%
        141 bp
        0.3
        3518par23_S120_L003_R1_001_fastq_gz
        90.0%
        53%
        141 bp
        0.4
        3518par23_S120_L003_R2_001_fastq_gz
        87.8%
        53%
        141 bp
        0.4
        3518par23_S120_L004_R1_001_fastq_gz
        89.9%
        53%
        140 bp
        0.3
        3518par23_S120_L004_R2_001_fastq_gz
        87.1%
        53%
        141 bp
        0.3
        3519par23_S119_L001_R1_001_fastq_gz
        91.0%
        51%
        140 bp
        0.6
        3519par23_S119_L001_R2_001_fastq_gz
        88.4%
        51%
        140 bp
        0.6
        3519par23_S119_L002_R1_001_fastq_gz
        91.0%
        51%
        140 bp
        0.5
        3519par23_S119_L002_R2_001_fastq_gz
        88.1%
        51%
        140 bp
        0.5
        3519par23_S119_L003_R1_001_fastq_gz
        91.1%
        51%
        140 bp
        0.6
        3519par23_S119_L003_R2_001_fastq_gz
        88.7%
        51%
        140 bp
        0.6
        3519par23_S119_L004_R1_001_fastq_gz
        91.1%
        51%
        140 bp
        0.5
        3519par23_S119_L004_R2_001_fastq_gz
        88.2%
        51%
        140 bp
        0.5
        3520par23_S121_L001_R1_001_fastq_gz
        89.8%
        51%
        140 bp
        0.4
        3520par23_S121_L001_R2_001_fastq_gz
        87.4%
        50%
        140 bp
        0.4
        3520par23_S121_L002_R1_001_fastq_gz
        89.7%
        51%
        140 bp
        0.4
        3520par23_S121_L002_R2_001_fastq_gz
        87.2%
        50%
        141 bp
        0.4
        3520par23_S121_L003_R1_001_fastq_gz
        89.9%
        51%
        140 bp
        0.4
        3520par23_S121_L003_R2_001_fastq_gz
        87.8%
        50%
        141 bp
        0.4
        3520par23_S121_L004_R1_001_fastq_gz
        89.8%
        51%
        140 bp
        0.4
        3520par23_S121_L004_R2_001_fastq_gz
        87.3%
        50%
        140 bp
        0.4
        3521par23_S122_L001_R1_001_fastq_gz
        88.1%
        54%
        138 bp
        0.3
        3521par23_S122_L001_R2_001_fastq_gz
        86.0%
        54%
        139 bp
        0.3
        3521par23_S122_L002_R1_001_fastq_gz
        87.9%
        54%
        138 bp
        0.3
        3521par23_S122_L002_R2_001_fastq_gz
        85.7%
        54%
        139 bp
        0.3
        3521par23_S122_L003_R1_001_fastq_gz
        88.2%
        54%
        138 bp
        0.3
        3521par23_S122_L003_R2_001_fastq_gz
        86.4%
        54%
        139 bp
        0.3
        3521par23_S122_L004_R1_001_fastq_gz
        87.9%
        54%
        138 bp
        0.3
        3521par23_S122_L004_R2_001_fastq_gz
        85.7%
        54%
        138 bp
        0.3
        3522par23_S123_L001_R1_001_fastq_gz
        54.5%
        53%
        131 bp
        0.0
        3522par23_S123_L001_R2_001_fastq_gz
        56.0%
        53%
        132 bp
        0.0
        3522par23_S123_L002_R1_001_fastq_gz
        57.2%
        54%
        133 bp
        0.0
        3522par23_S123_L002_R2_001_fastq_gz
        54.8%
        54%
        133 bp
        0.0
        3522par23_S123_L003_R1_001_fastq_gz
        56.2%
        53%
        132 bp
        0.0
        3522par23_S123_L003_R2_001_fastq_gz
        55.9%
        53%
        132 bp
        0.0
        3522par23_S123_L004_R1_001_fastq_gz
        53.8%
        53%
        132 bp
        0.0
        3522par23_S123_L004_R2_001_fastq_gz
        52.4%
        53%
        132 bp
        0.0
        3523par23_S124_L001_R1_001_fastq_gz
        88.4%
        54%
        143 bp
        0.1
        3523par23_S124_L001_R2_001_fastq_gz
        85.6%
        54%
        143 bp
        0.1
        3523par23_S124_L002_R1_001_fastq_gz
        88.4%
        54%
        143 bp
        0.1
        3523par23_S124_L002_R2_001_fastq_gz
        85.4%
        54%
        143 bp
        0.1
        3523par23_S124_L003_R1_001_fastq_gz
        88.4%
        54%
        143 bp
        0.1
        3523par23_S124_L003_R2_001_fastq_gz
        86.0%
        54%
        143 bp
        0.1
        3523par23_S124_L004_R1_001_fastq_gz
        88.3%
        54%
        143 bp
        0.1
        3523par23_S124_L004_R2_001_fastq_gz
        85.4%
        54%
        143 bp
        0.1
        3524par23_S125_L001_R1_001_fastq_gz
        89.9%
        51%
        143 bp
        0.3
        3524par23_S125_L001_R2_001_fastq_gz
        87.4%
        51%
        143 bp
        0.3
        3524par23_S125_L002_R1_001_fastq_gz
        89.7%
        51%
        143 bp
        0.3
        3524par23_S125_L002_R2_001_fastq_gz
        87.0%
        51%
        143 bp
        0.3
        3524par23_S125_L003_R1_001_fastq_gz
        90.0%
        52%
        143 bp
        0.3
        3524par23_S125_L003_R2_001_fastq_gz
        87.8%
        51%
        143 bp
        0.3
        3524par23_S125_L004_R1_001_fastq_gz
        89.8%
        51%
        143 bp
        0.3
        3524par23_S125_L004_R2_001_fastq_gz
        87.2%
        51%
        143 bp
        0.3
        3525par23_S126_L001_R1_001_fastq_gz
        68.5%
        51%
        58 bp
        0.0
        3525par23_S126_L001_R2_001_fastq_gz
        67.0%
        50%
        61 bp
        0.0
        3525par23_S126_L002_R1_001_fastq_gz
        67.6%
        51%
        59 bp
        0.0
        3525par23_S126_L002_R2_001_fastq_gz
        65.9%
        50%
        61 bp
        0.0
        3525par23_S126_L003_R1_001_fastq_gz
        68.3%
        51%
        59 bp
        0.0
        3525par23_S126_L003_R2_001_fastq_gz
        67.7%
        51%
        60 bp
        0.0
        3525par23_S126_L004_R1_001_fastq_gz
        67.8%
        51%
        59 bp
        0.0
        3525par23_S126_L004_R2_001_fastq_gz
        66.2%
        50%
        61 bp
        0.0
        3526par23_S127_L001_R1_001_fastq_gz
        89.6%
        49%
        145 bp
        0.4
        3526par23_S127_L001_R2_001_fastq_gz
        87.6%
        49%
        146 bp
        0.4
        3526par23_S127_L002_R1_001_fastq_gz
        89.5%
        49%
        146 bp
        0.3
        3526par23_S127_L002_R2_001_fastq_gz
        87.3%
        49%
        146 bp
        0.3
        3526par23_S127_L003_R1_001_fastq_gz
        89.8%
        49%
        146 bp
        0.4
        3526par23_S127_L003_R2_001_fastq_gz
        88.0%
        49%
        146 bp
        0.4
        3526par23_S127_L004_R1_001_fastq_gz
        89.6%
        49%
        145 bp
        0.4
        3526par23_S127_L004_R2_001_fastq_gz
        87.4%
        49%
        145 bp
        0.4
        3578par23_S128_L001_R1_001_fastq_gz
        92.1%
        51%
        144 bp
        0.7
        3578par23_S128_L001_R2_001_fastq_gz
        89.6%
        51%
        145 bp
        0.7
        3578par23_S128_L002_R1_001_fastq_gz
        92.0%
        51%
        144 bp
        0.6
        3578par23_S128_L002_R2_001_fastq_gz
        89.3%
        51%
        145 bp
        0.6
        3578par23_S128_L003_R1_001_fastq_gz
        92.2%
        51%
        144 bp
        0.7
        3578par23_S128_L003_R2_001_fastq_gz
        90.0%
        51%
        145 bp
        0.7
        3578par23_S128_L004_R1_001_fastq_gz
        92.2%
        51%
        144 bp
        0.7
        3578par23_S128_L004_R2_001_fastq_gz
        89.4%
        51%
        145 bp
        0.7
        3579par23_S129_L001_R1_001_fastq_gz
        88.0%
        52%
        131 bp
        0.3
        3579par23_S129_L001_R2_001_fastq_gz
        85.3%
        52%
        132 bp
        0.3
        3579par23_S129_L002_R1_001_fastq_gz
        87.9%
        53%
        132 bp
        0.3
        3579par23_S129_L002_R2_001_fastq_gz
        85.0%
        52%
        132 bp
        0.3
        3579par23_S129_L003_R1_001_fastq_gz
        88.2%
        53%
        132 bp
        0.3
        3579par23_S129_L003_R2_001_fastq_gz
        85.8%
        52%
        132 bp
        0.3
        3579par23_S129_L004_R1_001_fastq_gz
        88.0%
        53%
        131 bp
        0.3
        3579par23_S129_L004_R2_001_fastq_gz
        85.1%
        52%
        132 bp
        0.3
        3580par23_S130_L001_R1_001_fastq_gz
        87.2%
        53%
        140 bp
        0.1
        3580par23_S130_L001_R2_001_fastq_gz
        84.0%
        53%
        140 bp
        0.1
        3580par23_S130_L002_R1_001_fastq_gz
        86.9%
        53%
        140 bp
        0.1
        3580par23_S130_L002_R2_001_fastq_gz
        83.6%
        53%
        140 bp
        0.1
        3580par23_S130_L003_R1_001_fastq_gz
        87.3%
        53%
        140 bp
        0.1
        3580par23_S130_L003_R2_001_fastq_gz
        84.4%
        53%
        140 bp
        0.1
        3580par23_S130_L004_R1_001_fastq_gz
        87.1%
        53%
        140 bp
        0.1
        3580par23_S130_L004_R2_001_fastq_gz
        83.9%
        53%
        140 bp
        0.1
        3581par23_S131_L001_R1_001_fastq_gz
        92.3%
        50%
        144 bp
        0.8
        3581par23_S131_L001_R2_001_fastq_gz
        89.5%
        50%
        144 bp
        0.8
        3581par23_S131_L002_R1_001_fastq_gz
        92.2%
        50%
        144 bp
        0.7
        3581par23_S131_L002_R2_001_fastq_gz
        89.3%
        50%
        144 bp
        0.7
        3581par23_S131_L003_R1_001_fastq_gz
        92.4%
        50%
        144 bp
        0.8
        3581par23_S131_L003_R2_001_fastq_gz
        89.9%
        50%
        144 bp
        0.8
        3581par23_S131_L004_R1_001_fastq_gz
        92.2%
        50%
        143 bp
        0.8
        3581par23_S131_L004_R2_001_fastq_gz
        89.4%
        50%
        144 bp
        0.8
        3582par23_S132_L001_R1_001_fastq_gz
        88.8%
        52%
        145 bp
        0.1
        3582par23_S132_L001_R2_001_fastq_gz
        85.8%
        52%
        145 bp
        0.1
        3582par23_S132_L002_R1_001_fastq_gz
        88.7%
        52%
        145 bp
        0.1
        3582par23_S132_L002_R2_001_fastq_gz
        85.6%
        52%
        145 bp
        0.1
        3582par23_S132_L003_R1_001_fastq_gz
        89.3%
        52%
        145 bp
        0.1
        3582par23_S132_L003_R2_001_fastq_gz
        86.2%
        52%
        145 bp
        0.1
        3582par23_S132_L004_R1_001_fastq_gz
        89.0%
        52%
        145 bp
        0.1
        3582par23_S132_L004_R2_001_fastq_gz
        85.8%
        52%
        145 bp
        0.1
        3583par23_S133_L001_R1_001_fastq_gz
        86.2%
        52%
        124 bp
        0.3
        3583par23_S133_L001_R2_001_fastq_gz
        83.8%
        52%
        125 bp
        0.3
        3583par23_S133_L002_R1_001_fastq_gz
        86.0%
        52%
        125 bp
        0.3
        3583par23_S133_L002_R2_001_fastq_gz
        83.5%
        52%
        125 bp
        0.3
        3583par23_S133_L003_R1_001_fastq_gz
        86.3%
        52%
        125 bp
        0.3
        3583par23_S133_L003_R2_001_fastq_gz
        84.1%
        52%
        125 bp
        0.3
        3583par23_S133_L004_R1_001_fastq_gz
        85.9%
        52%
        124 bp
        0.3
        3583par23_S133_L004_R2_001_fastq_gz
        83.5%
        52%
        125 bp
        0.3
        3584par23_S134_L001_R1_001_fastq_gz
        88.6%
        53%
        139 bp
        0.2
        3584par23_S134_L001_R2_001_fastq_gz
        86.3%
        53%
        139 bp
        0.2
        3584par23_S134_L002_R1_001_fastq_gz
        88.4%
        54%
        139 bp
        0.2
        3584par23_S134_L002_R2_001_fastq_gz
        86.3%
        53%
        139 bp
        0.2
        3584par23_S134_L003_R1_001_fastq_gz
        88.8%
        54%
        139 bp
        0.2
        3584par23_S134_L003_R2_001_fastq_gz
        86.9%
        53%
        140 bp
        0.2
        3584par23_S134_L004_R1_001_fastq_gz
        88.5%
        54%
        139 bp
        0.2
        3584par23_S134_L004_R2_001_fastq_gz
        86.3%
        53%
        139 bp
        0.2
        3585par23_S135_L001_R1_001_fastq_gz
        90.3%
        52%
        144 bp
        0.3
        3585par23_S135_L001_R2_001_fastq_gz
        87.3%
        52%
        144 bp
        0.3
        3585par23_S135_L002_R1_001_fastq_gz
        90.2%
        52%
        144 bp
        0.3
        3585par23_S135_L002_R2_001_fastq_gz
        87.1%
        52%
        144 bp
        0.3
        3585par23_S135_L003_R1_001_fastq_gz
        90.4%
        52%
        144 bp
        0.3
        3585par23_S135_L003_R2_001_fastq_gz
        87.7%
        52%
        144 bp
        0.3
        3585par23_S135_L004_R1_001_fastq_gz
        90.2%
        52%
        144 bp
        0.3
        3585par23_S135_L004_R2_001_fastq_gz
        87.0%
        52%
        144 bp
        0.3

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..